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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gemma.R.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gemma.R_3.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gemma.R.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* this is package ‘gemma.R’ version ‘3.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gemma.R’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                              user system elapsed
get_dataset_object                           9.219  0.243  15.680
get_gene_differential_expression_values      2.477  0.159   9.768
dot-get_gene_differential_expression_values  2.518  0.115  11.311
get_dataset_processed_expression             1.154  0.067  14.117
get_dataset_raw_expression                   1.062  0.024  10.894
get_dataset_expression                       0.949  0.032   6.852
update_result                                0.684  0.019  33.865
get_dataset_differential_expression_analyses 0.598  0.008   7.433
get_differential_expression_values           0.245  0.024   5.103
get_datasets                                 0.191  0.016  10.906
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   18. │ └─gemma.R (local) FUN(X[[i]], ...)
   19. │   └─gemma.R::get_result_sets(datasets = experiment.ID, raw = TRUE)
   20. │     └─gemma.R:::.body(...)
   21. │       ├─base::eval(requestExpr)
   22. │       │ └─base::eval(requestExpr)
   23. │       └─httr::GET(...)
   24. │         └─httr:::request_perform(req, hu$handle$handle)
   25. │           ├─httr:::request_fetch(req$output, req$url, handle)
   26. │           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   27. │             └─curl::curl_fetch_memory(url, handle = handle)
   28. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 176 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/gemma.R.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL gemma.R
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘gemma.R’ ...
** this is package ‘gemma.R’ version ‘3.6.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gemma.R)

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(dplyr)

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 
> # Prevent certificate issues for GitHub actions
> options(gemma.SSL = FALSE)
> # get gemma api path if it's set in the environment
> gemma.R:::setGemmaPath('prod')
[1] "https://gemma.msl.ubc.ca/rest/v2/"
> print(gemma.R:::gemmaPath())
[1] "https://gemma.msl.ubc.ca/rest/v2/"
> test_check("gemma.R")
Loading required package: gemma.R
Warning: stack imbalance in '::', 130 then 132
Warning: stack imbalance in '{', 126 then 128
Warning: stack imbalance in 'lapply', 115 then 117
[ FAIL 1 | WARN 0 | SKIP 5 | PASS 176 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On Bioconductor (4): 'testCaches.R:37:3', 'testConvenience.R:15:5',
  'testConvenience.R:37:5', 'testDatasetEndpoints.R:88:5'
• empty test (1): 'testConvenience.R:1:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testOrderSanity.R:95:9'): Multiple sanity checks for expression/differential expression values and sample metadata ──
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [gemma.msl.ubc.ca]:
Operation too slow. Less than 1 bytes/sec transferred the last 600 seconds
Backtrace:
     ▆
  1. ├─gemma.R::get_differential_expression_values(dt) at testOrderSanity.R:95:9
  2. │ └─base::lapply(...)
  3. │   └─gemma.R (local) FUN(X[[i]], ...)
  4. │     └─gemma.R:::.getResultSets(x, memoised = memoised)
  5. │       ├─gemma.R:::.body(...)
  6. │       │ └─base::eval(quote(eval(preprocessor)(mData)), envir = envWhere)
  7. │       │   └─base::eval(quote(eval(preprocessor)(mData)), envir = envWhere)
  8. │       └─eval(preprocessor)(mData)
  9. │         └─gemma.R:::processDEMatrix(ret)
 10. │           └─gemma.R::get_result_sets(resultSets = parent.frame(n = 2)$resultSet)
 11. │             ├─gemma.R:::.body(...)
 12. │             │ └─base::eval(quote(eval(preprocessor)(mData)), envir = envWhere)
 13. │             │   └─base::eval(quote(eval(preprocessor)(mData)), envir = envWhere)
 14. │             └─eval(preprocessor)(mData)
 15. │               └─... %>% do.call(rbind, .)
 16. ├─base::do.call(rbind, .)
 17. ├─base::lapply(...)
 18. │ └─gemma.R (local) FUN(X[[i]], ...)
 19. │   └─gemma.R::get_result_sets(datasets = experiment.ID, raw = TRUE)
 20. │     └─gemma.R:::.body(...)
 21. │       ├─base::eval(requestExpr)
 22. │       │ └─base::eval(requestExpr)
 23. │       └─httr::GET(...)
 24. │         └─httr:::request_perform(req, hu$handle$handle)
 25. │           ├─httr:::request_fetch(req$output, req$url, handle)
 26. │           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 27. │             └─curl::curl_fetch_memory(url, handle = handle)
 28. └─curl:::raise_libcurl_error(...)

[ FAIL 1 | WARN 0 | SKIP 5 | PASS 176 ]
Error: Test failures
Execution halted